TB-Profiler result

Run: ERR4812971
Summary

Run ID: ERR4812971

Sample name:

Date: 20-10-2023 05:04:16

Number of reads: 1018970

Percentage reads mapped: 99.55

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Asp435Val (0.49), rpoB p.His445Asn (0.51)
Isoniazid R katG p.Ser315Thr (0.86)
Ethambutol R embB p.Met306Ile (0.38), embB p.Tyr319Ser (0.50)
Pyrazinamide R pncA p.Gly132Ser (0.30), pncA p.Gln10Arg (0.51)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.58)
Moxifloxacin R gyrA p.Ala90Val (0.58)
Ofloxacin R gyrA p.Ala90Val (0.58)
Levofloxacin R gyrA p.Ala90Val (0.58)
Ciprofloxacin R gyrA p.Ala90Val (0.58)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7570 p.Ala90Val missense_variant 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.49 rifampicin
rpoB 761139 p.His445Asn missense_variant 0.51 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid
pncA 2288848 p.Gly132Ser missense_variant 0.3 pyrazinamide
pncA 2289213 p.Gln10Arg missense_variant 0.51 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.38 ethambutol
embB 4247469 p.Tyr319Ser missense_variant 0.5 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 0.52
gid 4408156 p.Leu16Arg missense_variant 1.0